We present a method for the analysis of functional properties of large-scale
DNA strand displacement (DSD) circuits based on Satisfiability Modulo Theories
that enables us to prove the functional correctness of DNA circuit designs for
arbitrary inputs, and provides significantly improved scalability and
expressivity over existing methods. We implement this method as an extension to
the Visual DSD tool, and use it to formalize the behavior of a 4-bit square root
circuit, together with the components used for its construction. We show that our
method successfully verifies that certain designs function as required and
identifies erroneous computations in others, even when millions of copies of a
circuit are interacting with each other in parallel. Our method is also
applicable in the verification of properties for more general chemical reaction
networks.